bash profile complete bash-4.2$ pwd /home/dlk2148 bash-4.2$ cd ./staging/daniel/fmriprep/fmriprep_job1.sh bash: cd: ./staging/daniel/fmriprep/fmriprep_job1.sh: No such file or directory bash-4.2$ cd mnt/ bash-4.2$ ls labshare locker staging bash-4.2$ ./staging/daniel/fmriprep/fmriprep_job1.sh RUNNING: docker run --rm -it -v /home/dlk2148/mnt/staging/daniel/fmriprep/freesurfer_license.txt:/opt/freesurfer/license.txt:ro -v /home/dlk2148/mnt/labshare/daniel/BIDS:/data:ro -v /home/dlk2148/mnt/labshare/daniel/fmriprep/out:/out -v /home/dlk2148/mnt/labshare/daniel/fmriprep/work:/scratch poldracklab/fmriprep:1.0.13 /data /out participant --no-submm-recon --ignore slicetiming --participant_label 18042401 -w /scratch 180710-21:49:32,347 workflow IMPORTANT: Running fMRIPREP version 1.0.13: * BIDS dataset path: /data. * Participant list: ['18042401']. * Run identifier: 20180710-214932_608acd26-7ea2-40ac-a192-56ff5401dac0. 180710-21:49:33,845 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context011_run-01_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.23 GB. 180710-21:49:34,496 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context011_run-01_bold.nii.gz found. 180710-21:49:35,194 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:36,830 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context011_run-02_bold.nii.gz" (0.32 GB / 286 TRs). Memory resampled/largemem=1.30/2.23 GB. 180710-21:49:37,448 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context011_run-02_bold.nii.gz found. 180710-21:49:38,143 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:39,830 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context021_run-01_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.23 GB. 180710-21:49:40,373 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context021_run-01_bold.nii.gz found. 180710-21:49:41,71 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:42,751 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context021_run-02_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.23 GB. 180710-21:49:43,397 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context021_run-02_bold.nii.gz found. 180710-21:49:44,93 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:45,796 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context031_run-01_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.23 GB. 180710-21:49:46,310 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context031_run-01_bold.nii.gz found. 180710-21:49:47,3 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:48,699 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context031_run-02_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.24 GB. 180710-21:49:49,247 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context031_run-02_bold.nii.gz found. 180710-21:49:49,939 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:51,642 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context041_run-01_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.31/2.24 GB. 180710-21:49:52,173 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context041_run-01_bold.nii.gz found. 180710-21:49:52,873 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:54,592 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context041_run-02_bold.nii.gz" (0.33 GB / 286 TRs). Memory resampled/largemem=1.30/2.24 GB. 180710-21:49:55,145 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-context041_run-02_bold.nii.gz found. 180710-21:49:55,834 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:49:57,442 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-localizer_run-01_bold.nii.gz" (0.25 GB / 223 TRs). Memory resampled/largemem=1.02/1.58 GB. 180710-21:49:58,155 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-localizer_run-01_bold.nii.gz found. 180710-21:49:58,852 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:50:00,418 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-resting_run-01_bold.nii.gz" (0.44 GB / 387 TRs). Memory resampled/largemem=1.76/3.47 GB. 180710-21:50:00,937 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-resting_run-01_bold.nii.gz found. 180710-21:50:01,637 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:50:03,409 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-resting_run-02_bold.nii.gz" (0.44 GB / 387 TRs). Memory resampled/largemem=1.77/3.47 GB. 180710-21:50:03,928 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-18042401/ses-01/func/sub-18042401_ses-01_task-resting_run-02_bold.nii.gz found. 180710-21:50:04,624 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180710-21:50:15,758 sentry.errors ERROR: Sentry responded with an error: (url: https://sentry.io/api/1137693/store/) Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/urllib/request.py", line 1318, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/usr/local/miniconda/lib/python3.6/http/client.py", line 1239, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/local/miniconda/lib/python3.6/http/client.py", line 1285, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/local/miniconda/lib/python3.6/http/client.py", line 1234, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/local/miniconda/lib/python3.6/http/client.py", line 1026, in _send_output self.send(msg) File "/usr/local/miniconda/lib/python3.6/http/client.py", line 964, in send self.connect() File "/usr/local/miniconda/lib/python3.6/site-packages/raven/utils/http.py", line 31, in connect timeout=self.timeout, File "/usr/local/miniconda/lib/python3.6/socket.py", line 724, in create_connection raise err File "/usr/local/miniconda/lib/python3.6/socket.py", line 713, in create_connection sock.connect(sa) socket.timeout: timed out During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/raven/transport/threaded.py", line 165, in send_sync super(ThreadedHTTPTransport, self).send(url, data, headers) File "/usr/local/miniconda/lib/python3.6/site-packages/raven/transport/http.py", line 43, in send ca_certs=self.ca_certs, File "/usr/local/miniconda/lib/python3.6/site-packages/raven/utils/http.py", line 66, in urlopen return opener.open(url, data, timeout) File "/usr/local/miniconda/lib/python3.6/urllib/request.py", line 526, in open response = self._open(req, data) File "/usr/local/miniconda/lib/python3.6/urllib/request.py", line 544, in _open '_open', req) File "/usr/local/miniconda/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(*args) File "/usr/local/miniconda/lib/python3.6/site-packages/raven/utils/http.py", line 46, in https_open return self.do_open(ValidHTTPSConnection, req) File "/usr/local/miniconda/lib/python3.6/urllib/request.py", line 1320, in do_open raise URLError(err) urllib.error.URLError: 180710-21:50:15,924 sentry.errors.uncaught ERROR: ['fMRIPrep running'] 180710-21:59:01,299 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/recon_config". 180710-21:59:01,355 workflow INFO: [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs") 180710-21:59:01,402 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.recon_config". 180710-21:59:21,203 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon1". 180710-21:59:21,302 workflow INFO: [Node] Running "autorecon1" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon1 -i /data/sub-18042401/ses-01/anat/sub-18042401_ses-01_T1w.nii.gz -noskullstrip -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180710-22:05:52,683 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon1". 180710-22:05:54,256 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm". 180710-22:05:54,297 workflow INFO: [Node] Running "fsnative_2_t1_xfm" ("niworkflows.nipype.interfaces.freesurfer.preprocess.RobustRegister"), a CommandLine Interface with command: mri_robust_register --satit --iscale --lta /scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /out/freesurfer/sub-18042401/mri/T1.mgz --dst /data/sub-18042401/ses-01/anat/sub-18042401_ses-01_T1w.nii.gz 180710-22:06:00,942 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". 180710-22:06:00,979 workflow INFO: [Node] Running "skull_strip_extern" ("fmriprep.interfaces.freesurfer.FSInjectBrainExtracted") 180710-22:06:03,353 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". 180710-22:06:36,261 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". 180710-22:06:36,341 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180710-22:06:36,346 workflow INFO: [Node] Running "autorecon2_vol" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180710-22:06:36,349 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180710-22:06:48,733 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm". 180710-22:06:50,276 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm". 180710-22:06:50,329 workflow INFO: [Node] Running "t1_2_fsnative_xfm" ("niworkflows.nipype.interfaces.freesurfer.utils.LTAConvert"), a CommandLine Interface with command: lta_convert --inlta /scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta 180710-22:06:50,421 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm". 180710-22:06:52,259 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk". 180710-22:06:52,298 workflow INFO: [Node] Running "lta_2_itk" ("niworkflows.nipype.interfaces.freesurfer.utils.LTAConvert"), a CommandLine Interface with command: lta_convert --inlta /scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt 180710-22:06:52,388 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk". 180711-00:52:00,152 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol". 180711-00:52:03,317 workflow INFO: [Node] Setting-up "_autorecon_surfs0" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". 180711-00:52:03,391 interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-00:52:03,396 workflow INFO: [Node] Running "_autorecon_surfs0" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-00:52:03,398 interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-01:20:40,56 workflow WARNING: [Node] Error on "_autorecon_surfs0" (/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0) 180711-01:20:40,414 workflow ERROR: Node _autorecon_surfs0 failed to run on host ef810ab26e4e. 180711-01:20:40,434 workflow ERROR: Saving crash info to /out/fmriprep/sub-18042401/log/20180710-214932_608acd26-7ea2-40ac-a192-56ff5401dac0/crash-20180711-012040-root-_autorecon_surfs0-1ba321e0-b7c1-429e-8f0d-038f546bbe3f.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 480, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 564, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 644, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 520, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1020, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 957, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux ef810ab26e4e 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-18042401/scripts/recon-all.local-copy' #-------------------------------------------- #@# Tessellate lh Wed Jul 11 00:52:04 UTC 2018 /out/freesurfer/sub-18042401/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 268723: 0.001861) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 178 vertices, 209 faces slice 40: 4211 vertices, 4405 faces slice 50: 11361 vertices, 11667 faces slice 60: 21148 vertices, 21506 faces slice 70: 32307 vertices, 32698 faces slice 80: 43771 vertices, 44150 faces slice 90: 55540 vertices, 55943 faces slice 100: 67119 vertices, 67545 faces slice 110: 78927 vertices, 79367 faces slice 120: 89572 vertices, 89960 faces slice 130: 100225 vertices, 100632 faces slice 140: 110430 vertices, 110755 faces slice 150: 118676 vertices, 118974 faces slice 160: 125463 vertices, 125729 faces slice 170: 131745 vertices, 131990 faces slice 180: 136844 vertices, 137078 faces slice 190: 140818 vertices, 140966 faces slice 200: 141486 vertices, 141532 faces slice 210: 141486 vertices, 141532 faces slice 220: 141486 vertices, 141532 faces slice 230: 141486 vertices, 141532 faces slice 240: 141486 vertices, 141532 faces slice 250: 141486 vertices, 141532 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 141486 voxel in cpt #1: X=-46 [v=141486,e=424596,f=283064] located at (-28.770231, -23.594574, 24.799118) For the whole surface: X=-46 [v=141486,e=424596,f=283064] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Jul 11 00:52:08 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Jul 11 00:52:13 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.8 mm, total surface area = 74595 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.153 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 43.809497 mris_inflate stimesec 0.222788 mris_inflate ru_maxrss 214416 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 53805 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9960 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5151 mris_inflate ru_nivcsw 787 #-------------------------------------------- #@# QSphere lh Wed Jul 11 00:52:33 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->7.40) (max @ vno 56251 --> 56273) face area 0.02 +- 0.03 (-0.18-->0.71) == Number of threads available to mris_sphere for OpenMP = 3 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.143, avgs=0 005/300: dt: 0.9000, rms radial error=176.884, avgs=0 010/300: dt: 0.9000, rms radial error=176.327, avgs=0 015/300: dt: 0.9000, rms radial error=175.596, avgs=0 020/300: dt: 0.9000, rms radial error=174.763, avgs=0 025/300: dt: 0.9000, rms radial error=173.872, avgs=0 030/300: dt: 0.9000, rms radial error=172.949, avgs=0 035/300: dt: 0.9000, rms radial error=172.008, avgs=0 040/300: dt: 0.9000, rms radial error=171.060, avgs=0 045/300: dt: 0.9000, rms radial error=170.109, avgs=0 050/300: dt: 0.9000, rms radial error=169.160, avgs=0 055/300: dt: 0.9000, rms radial error=168.213, avgs=0 060/300: dt: 0.9000, rms radial error=167.270, avgs=0 065/300: dt: 0.9000, rms radial error=166.331, avgs=0 070/300: dt: 0.9000, rms radial error=165.397, avgs=0 075/300: dt: 0.9000, rms radial error=164.468, avgs=0 080/300: dt: 0.9000, rms radial error=163.543, avgs=0 085/300: dt: 0.9000, rms radial error=162.624, avgs=0 090/300: dt: 0.9000, rms radial error=161.709, avgs=0 095/300: dt: 0.9000, rms radial error=160.800, avgs=0 100/300: dt: 0.9000, rms radial error=159.895, avgs=0 105/300: dt: 0.9000, rms radial error=158.995, avgs=0 110/300: dt: 0.9000, rms radial error=158.100, avgs=0 115/300: dt: 0.9000, rms radial error=157.210, avgs=0 120/300: dt: 0.9000, rms radial error=156.325, avgs=0 125/300: dt: 0.9000, rms radial error=155.445, avgs=0 130/300: dt: 0.9000, rms radial error=154.569, avgs=0 135/300: dt: 0.9000, rms radial error=153.698, avgs=0 140/300: dt: 0.9000, rms radial error=152.832, avgs=0 145/300: dt: 0.9000, rms radial error=151.970, avgs=0 150/300: dt: 0.9000, rms radial error=151.113, avgs=0 155/300: dt: 0.9000, rms radial error=150.261, avgs=0 160/300: dt: 0.9000, rms radial error=149.413, avgs=0 165/300: dt: 0.9000, rms radial error=148.570, avgs=0 170/300: dt: 0.9000, rms radial error=147.731, avgs=0 175/300: dt: 0.9000, rms radial error=146.897, avgs=0 180/300: dt: 0.9000, rms radial error=146.068, avgs=0 185/300: dt: 0.9000, rms radial error=145.244, avgs=0 190/300: dt: 0.9000, rms radial error=144.424, avgs=0 195/300: dt: 0.9000, rms radial error=143.609, avgs=0 200/300: dt: 0.9000, rms radial error=142.798, avgs=0 205/300: dt: 0.9000, rms radial error=141.992, avgs=0 210/300: dt: 0.9000, rms radial error=141.190, avgs=0 215/300: dt: 0.9000, rms radial error=140.392, avgs=0 220/300: dt: 0.9000, rms radial error=139.599, avgs=0 225/300: dt: 0.9000, rms radial error=138.811, avgs=0 230/300: dt: 0.9000, rms radial error=138.027, avgs=0 235/300: dt: 0.9000, rms radial error=137.247, avgs=0 240/300: dt: 0.9000, rms radial error=136.471, avgs=0 245/300: dt: 0.9000, rms radial error=135.700, avgs=0 250/300: dt: 0.9000, rms radial error=134.933, avgs=0 255/300: dt: 0.9000, rms radial error=134.171, avgs=0 260/300: dt: 0.9000, rms radial error=133.413, avgs=0 265/300: dt: 0.9000, rms radial error=132.659, avgs=0 270/300: dt: 0.9000, rms radial error=131.909, avgs=0 275/300: dt: 0.9000, rms radial error=131.163, avgs=0 280/300: dt: 0.9000, rms radial error=130.422, avgs=0 285/300: dt: 0.9000, rms radial error=129.685, avgs=0 290/300: dt: 0.9000, rms radial error=128.952, avgs=0 295/300: dt: 0.9000, rms radial error=128.223, avgs=0 300/300: dt: 0.9000, rms radial error=127.498, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16782.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2872.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 315.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00722 epoch 4 (K=640.0), pass 1, starting sse = 20.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00814 final distance error %27.90 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 253.260648 mris_sphere stimesec 0.410882 mris_sphere ru_maxrss 214884 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 53867 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9960 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 6142 mris_sphere ru_nivcsw 3264 FSRUNTIME@ mris_sphere 0.0338 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Wed Jul 11 00:54:35 UTC 2018 /out/freesurfer/sub-18042401/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #@# Fix Topology lh Wed Jul 11 00:54:35 UTC 2018 mris_fix_topology -rusage /out/freesurfer/sub-18042401/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-18042401 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-46 (nv=141486, nf=283064, ne=424596, g=24) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 4622 ambiguous faces found in tessellation segmenting defects... 37 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 15 into 14 36 defects to be corrected 0 vertices coincident reading input surface /out/freesurfer/sub-18042401/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1040 (-4.5520) -vertex loglikelihood: -5.6889 (-2.8445) -normal dot loglikelihood: -3.6112 (-3.6112) -quad curv loglikelihood: -6.3072 (-3.1536) Total Loglikelihood : -24.7113 CORRECTING DEFECT 0 (vertices=221, convex hull=163, v0=292) After retessellation of defect 0 (v0=292), euler #=-33 (138772,415494,276689) : difference with theory (-33) = 0 CORRECTING DEFECT 1 (vertices=37, convex hull=61, v0=35325) After retessellation of defect 1 (v0=35325), euler #=-32 (138788,415567,276747) : difference with theory (-32) = 0 CORRECTING DEFECT 2 (vertices=17, convex hull=50, v0=35600) After retessellation of defect 2 (v0=35600), euler #=-31 (138797,415611,276783) : difference with theory (-31) = 0 CORRECTING DEFECT 3 (vertices=8, convex hull=26, v0=41045) After retessellation of defect 3 (v0=41045), euler #=-30 (138799,415624,276795) : difference with theory (-30) = 0 CORRECTING DEFECT 4 (vertices=471, convex hull=228, v0=50261) After retessellation of defect 4 (v0=50261), euler #=-30 (138834,415848,276984) : difference with theory (-29) = 1 CORRECTING DEFECT 5 (vertices=59, convex hull=62, v0=53923) After retessellation of defect 5 (v0=53923), euler #=-29 (138843,415902,277030) : difference with theory (-28) = 1 CORRECTING DEFECT 6 (vertices=5, convex hull=22, v0=62173) After retessellation of defect 6 (v0=62173), euler #=-28 (138844,415911,277039) : difference with theory (-27) = 1 CORRECTING DEFECT 7 (vertices=22, convex hull=25, v0=85843) After retessellation of defect 7 (v0=85843), euler #=-27 (138848,415931,277056) : difference with theory (-26) = 1 CORRECTING DEFECT 8 (vertices=5, convex hull=17, v0=95554) After retessellation of defect 8 (v0=95554), euler #=-26 (138849,415938,277063) : difference with theory (-25) = 1 CORRECTING DEFECT 9 (vertices=16, convex hull=23, v0=96758) After retessellation of defect 9 (v0=96758), euler #=-25 (138852,415951,277074) : difference with theory (-24) = 1 CORRECTING DEFECT 10 (vertices=139, convex hull=118, v0=96827) After retessellation of defect 10 (v0=96827), euler #=-24 (138903,416153,277226) : difference with theory (-23) = 1 CORRECTING DEFECT 11 (vertices=181, convex hull=60, v0=96999) After retessellation of defect 11 (v0=96999), euler #=-23 (138916,416219,277280) : difference with theory (-22) = 1 CORRECTING DEFECT 12 (vertices=28, convex hull=46, v0=97814) After retessellation of defect 12 (v0=97814), euler #=-22 (138929,416275,277324) : difference with theory (-21) = 1 CORRECTING DEFECT 13 (vertices=54, convex hull=41, v0=98646) After retessellation of defect 13 (v0=98646), euler #=-21 (138938,416313,277354) : difference with theory (-20) = 1 CORRECTING DEFECT 14 (vertices=124, convex hull=115, v0=99915) After retessellation of defect 14 (v0=99915), euler #=-19 (138999,416551,277533) : difference with theory (-19) = 0 CORRECTING DEFECT 15 (vertices=770, convex hull=169, v0=102003) After retessellation of defect 15 (v0=102003), euler #=-18 (139011,416688,277659) : difference with theory (-18) = 0 CORRECTING DEFECT 16 (vertices=6, convex hull=22, v0=103334) After retessellation of defect 16 (v0=103334), euler #=-17 (139012,416697,277668) : difference with theory (-17) = 0 CORRECTING DEFECT 17 (vertices=7, convex hull=8, v0=105026) After retessellation of defect 17 (v0=105026), euler #=-16 (139013,416701,277672) : difference with theory (-16) = 0 CORRECTING DEFECT 18 (vertices=6, convex hull=34, v0=105081) After retessellation of defect 18 (v0=105081), euler #=-15 (139016,416720,277689) : difference with theory (-15) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=52, v0=106256) After retessellation of defect 19 (v0=106256), euler #=-14 (139025,416771,277732) : difference with theory (-14) = 0 CORRECTING DEFECT 20 (vertices=7, convex hull=26, v0=111014) After retessellation of defect 20 (v0=111014), euler #=-13 (139027,416785,277745) : difference with theory (-13) = 0 CORRECTING DEFECT 21 (vertices=37, convex hull=47, v0=111173) After retessellation of defect 21 (v0=111173), euler #=-12 (139038,416834,277784) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=20, convex hull=56, v0=112909) After retessellation of defect 22 (v0=112909), euler #=-11 (139046,416883,277826) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=13, convex hull=25, v0=112935) After retessellation of defect 23 (v0=112935), euler #=-10 (139049,416901,277842) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=158, convex hull=94, v0=115569) After retessellation of defect 24 (v0=115569), euler #=-9 (139091,417069,277969) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=29, convex hull=31, v0=116198) After retessellation of defect 25 (v0=116198), euler #=-8 (139097,417098,277993) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=23, convex hull=60, v0=117117) After retessellation of defect 26 (v0=117117), euler #=-7 (139109,417157,278041) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=23, convex hull=34, v0=119228) After retessellation of defect 27 (v0=119228), euler #=-6 (139112,417185,278067) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=18, convex hull=40, v0=119672) After retessellation of defect 28 (v0=119672), euler #=-5 (139120,417226,278101) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=38, convex hull=40, v0=124561) After retessellation of defect 29 (v0=124561), euler #=-4 (139129,417268,278135) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=20, convex hull=29, v0=126110) After retessellation of defect 30 (v0=126110), euler #=-3 (139134,417291,278154) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=31, convex hull=72, v0=131101) After retessellation of defect 31 (v0=131101), euler #=-2 (139154,417381,278225) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=11, convex hull=24, v0=133690) After retessellation of defect 32 (v0=133690), euler #=-1 (139155,417391,278235) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=38, convex hull=74, v0=139005) After retessellation of defect 33 (v0=139005), euler #=0 (139170,417466,278296) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=22, convex hull=17, v0=139954) After retessellation of defect 34 (v0=139954), euler #=1 (139171,417473,278303) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=51, convex hull=83, v0=141017) After retessellation of defect 35 (v0=141017), euler #=2 (139184,417546,278364) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.02-->13.76) (max @ vno 53435 --> 56991) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.02-->13.76) (max @ vno 53435 --> 56991) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 175 mutations (38.9%), 275 crossovers (61.1%), 299 vertices were eliminated building final representation... 2302 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139184, nf=278364, ne=417546, g=0) writing corrected surface to /out/freesurfer/sub-18042401/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.3 minutes 0 defective edges removing intersecting faces 000: 219 intersecting 001: 5 intersecting mris_fix_topology utimesec 1282.734614 mris_fix_topology stimesec 0.226995 mris_fix_topology ru_maxrss 438300 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 110570 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13128 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 2020 mris_fix_topology ru_nivcsw 1148 FSRUNTIME@ mris_fix_topology lh 0.3553 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 139184 - 417546 + 278364 = 2 --> 0 holes F =2V-4: 278364 = 278368-4 (0) 2E=3F: 835092 = 835092 (0) total defect index = 0 /out/freesurfer/sub-18042401/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 32 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jul 11 01:15:59 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-18042401 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /out/freesurfer/sub-18042401/mri/filled.mgz... reading volume /out/freesurfer/sub-18042401/mri/brain.finalsurfs.mgz... reading volume /out/freesurfer/sub-18042401/mri/../mri/aseg.presurf.mgz... reading volume /out/freesurfer/sub-18042401/mri/wm.mgz... 17340 bright wm thresholded. 20 bright non-wm voxels segmented. reading original surface position from /out/freesurfer/sub-18042401/surf/lh.orig... computing class statistics... border white: 263682 voxels (1.57%) border gray 287055 voxels (1.71%) WM (101.0): 100.8 +- 6.6 [70.0 --> 110.0] GM (81.0) : 79.7 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 57.8 (was 40) setting MAX_GRAY to 98.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->5.17) (max @ vno 53435 --> 56991) face area 0.28 +- 0.12 (0.00-->4.92) mean absolute distance = 0.77 +- 0.99 3788 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=77+-7.0 mean inside = 97.3, mean outside = 83.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=86.8, 48 (48) missing vertices, mean dist 0.3 [0.7 (%37.8)->0.8 (%62.2))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ef810, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.10-->6.57) (max @ vno 53435 --> 56991) face area 0.28 +- 0.13 (0.00-->5.25) mean absolute distance = 0.40 +- 0.66 3470 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2302961.0, rms=8.026 001: dt: 0.5000, sse=1403747.0, rms=5.622 (29.950%) 002: dt: 0.5000, sse=1000737.9, rms=4.083 (27.370%) 003: dt: 0.5000, sse=818053.9, rms=3.143 (23.024%) 004: dt: 0.5000, sse=732818.1, rms=2.597 (17.367%) 005: dt: 0.5000, sse=698728.8, rms=2.337 (10.023%) 006: dt: 0.5000, sse=684968.3, rms=2.217 (5.142%) rms = 2.18, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=681134.3, rms=2.177 (1.795%) 008: dt: 0.2500, sse=615802.9, rms=1.383 (36.460%) 009: dt: 0.2500, sse=607826.9, rms=1.261 (8.817%) rms = 1.23, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=606069.2, rms=1.234 (2.198%) rms = 1.22, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=604874.2, rms=1.216 (1.401%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.1, 28 (5) missing vertices, mean dist -0.2 [0.5 (%69.7)->0.3 (%30.3))] %77 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ef810, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.09-->6.81) (max @ vno 53435 --> 56991) face area 0.35 +- 0.16 (0.00-->7.87) mean absolute distance = 0.29 +- 0.42 3868 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1110065.2, rms=3.863 012: dt: 0.5000, sse=865548.2, rms=2.432 (37.060%) 013: dt: 0.5000, sse=803547.3, rms=1.917 (21.145%) 014: dt: 0.5000, sse=779345.6, rms=1.697 (11.484%) rms = 1.72, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=755769.1, rms=1.362 (19.745%) 016: dt: 0.2500, sse=743150.7, rms=1.159 (14.888%) 017: dt: 0.2500, sse=739901.6, rms=1.100 (5.146%) rms = 1.07, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=738252.4, rms=1.074 (2.357%) rms = 1.06, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=737789.2, rms=1.057 (1.575%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=91.1, 27 (3) missing vertices, mean dist -0.2 [0.3 (%72.1)->0.2 (%27.9))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ef810, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->6.97) (max @ vno 53435 --> 56991) face area 0.34 +- 0.16 (0.00-->8.34) mean absolute distance = 0.23 +- 0.34 3628 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=886887.1, rms=2.760 020: dt: 0.5000, sse=755008.6, rms=1.628 (41.030%) 021: dt: 0.5000, sse=743269.9, rms=1.507 (7.447%) rms = 1.46, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=737828.2, rms=1.463 (2.899%) 023: dt: 0.2500, sse=711804.1, rms=1.012 (30.821%) rms = 0.96, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=708169.1, rms=0.963 (4.888%) rms = 0.95, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=707430.2, rms=0.951 (1.235%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=91.8, 42 (3) missing vertices, mean dist -0.1 [0.2 (%58.8)->0.2 (%41.2))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ef810, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /out/freesurfer/sub-18042401/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=718755.8, rms=1.375 026: dt: 0.5000, sse=697209.0, rms=0.968 (29.621%) rms = 1.21, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=686015.0, rms=0.804 (16.895%) rms = 0.78, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=684958.9, rms=0.776 (3.528%) rms = 0.76, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=683110.9, rms=0.762 (1.835%) positioning took 0.4 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6734 vertices erasing segment 0 (vno[0] = 39601) erasing segment 1 (vno[0] = 39603) erasing segment 2 (vno[0] = 39689) erasing segment 4 (vno[0] = 73742) erasing segment 5 (vno[0] = 91184) erasing segment 6 (vno[0] = 102687) erasing segment 7 (vno[0] = 102799) erasing segment 8 (vno[0] = 103718) erasing segment 9 (vno[0] = 104727) erasing segment 10 (vno[0] = 107422) writing cortex label to /out/freesurfer/sub-18042401/label/lh.cortex.label... writing curvature file /out/freesurfer/sub-18042401/surf/lh.curv writing smoothed area to lh.area writing curvature file /out/freesurfer/sub-18042401/surf/lh.area vertex spacing 0.88 +- 0.24 (0.06-->7.23) (max @ vno 53435 --> 56991) face area 0.33 +- 0.16 (0.00-->8.01) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jul 11 01:20:12 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Jul 11 01:20:17 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_inflate -rusage /out/freesurfer/sub-18042401/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 47.0 mm, total surface area = 83625 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 43.158942 mris_inflate stimesec 0.352901 mris_inflate ru_maxrss 211056 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 52981 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10880 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2288 mris_inflate ru_nivcsw 487 #-------------------------------------------- #@# Curv .H and .K lh Wed Jul 11 01:20:37 UTC 2018 /out/freesurfer/sub-18042401/surf mris_curvature -w lh.white.preaparc total integrated curvature = 6.262*4pi (78.689) --> -5 handles ICI = 156.4, FI = 1653.4, variation=25908.129 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux ef810ab26e4e 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:20:39 UTC 2018 For more details, see the log file /out/freesurfer/sub-18042401/scripts/recon-all-lh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Standard error: ln: failed to create symbolic link 'lh.white.H': Operation not supported Return code: 1 180711-01:20:40,922 workflow INFO: [Node] Setting-up "_autorecon_surfs1" in "/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". 180711-01:20:40,972 interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-01:20:40,977 workflow INFO: [Node] Running "_autorecon_surfs1" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-01:20:40,980 interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer 180711-01:39:48,100 workflow WARNING: [Node] Error on "_autorecon_surfs1" (/scratch/fmriprep_wf/single_subject_18042401_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1) 180711-01:39:49,469 workflow ERROR: Node _autorecon_surfs1 failed to run on host ef810ab26e4e. 180711-01:39:49,473 workflow ERROR: Saving crash info to /out/fmriprep/sub-18042401/log/20180710-214932_608acd26-7ea2-40ac-a192-56ff5401dac0/crash-20180711-013949-root-_autorecon_surfs1-3dc6714d-809d-4af3-9d5a-d7bcb2c05847.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 480, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 564, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 644, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 520, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1020, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 957, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 3 -subjid sub-18042401 -sd /out/freesurfer Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux ef810ab26e4e 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-18042401/scripts/recon-all.local-copy' #-------------------------------------------- #@# Tessellate rh Wed Jul 11 01:20:41 UTC 2018 /out/freesurfer/sub-18042401/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 4 found - 4 modified | TOTAL: 4 pass 2 (yz+): 0 found - 4 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 6 (out of 267260: 0.002245) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 23 vertices, 30 faces slice 40: 3553 vertices, 3706 faces slice 50: 10265 vertices, 10538 faces slice 60: 19043 vertices, 19372 faces slice 70: 29977 vertices, 30384 faces slice 80: 42879 vertices, 43311 faces slice 90: 54194 vertices, 54634 faces slice 100: 66805 vertices, 67209 faces slice 110: 78958 vertices, 79333 faces slice 120: 90166 vertices, 90575 faces slice 130: 100609 vertices, 100977 faces slice 140: 109781 vertices, 110057 faces slice 150: 117123 vertices, 117367 faces slice 160: 124080 vertices, 124315 faces slice 170: 130104 vertices, 130316 faces slice 180: 135107 vertices, 135292 faces slice 190: 138524 vertices, 138634 faces slice 200: 139790 vertices, 139814 faces slice 210: 139790 vertices, 139814 faces slice 220: 139790 vertices, 139814 faces slice 230: 139790 vertices, 139814 faces slice 240: 139790 vertices, 139814 faces slice 250: 139790 vertices, 139814 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 139790 voxel in cpt #1: X=-24 [v=139790,e=419442,f=279628] located at (27.000902, -23.500479, 26.992325) For the whole surface: X=-24 [v=139790,e=419442,f=279628] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Jul 11 01:20:46 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Jul 11 01:20:51 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.6 mm, total surface area = 73941 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 43.067589 mris_inflate stimesec 0.322891 mris_inflate ru_maxrss 211916 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 53173 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9840 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2442 mris_inflate ru_nivcsw 644 #-------------------------------------------- #@# QSphere rh Wed Jul 11 01:21:10 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.57 (0.00-->6.82) (max @ vno 104024 --> 104025) face area 0.02 +- 0.03 (-0.24-->0.62) == Number of threads available to mris_sphere for OpenMP = 3 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.408, avgs=0 005/300: dt: 0.9000, rms radial error=177.147, avgs=0 010/300: dt: 0.9000, rms radial error=176.587, avgs=0 015/300: dt: 0.9000, rms radial error=175.852, avgs=0 020/300: dt: 0.9000, rms radial error=175.016, avgs=0 025/300: dt: 0.9000, rms radial error=174.123, avgs=0 030/300: dt: 0.9000, rms radial error=173.197, avgs=0 035/300: dt: 0.9000, rms radial error=172.255, avgs=0 040/300: dt: 0.9000, rms radial error=171.304, avgs=0 045/300: dt: 0.9000, rms radial error=170.351, avgs=0 050/300: dt: 0.9000, rms radial error=169.399, avgs=0 055/300: dt: 0.9000, rms radial error=168.449, avgs=0 060/300: dt: 0.9000, rms radial error=167.503, avgs=0 065/300: dt: 0.9000, rms radial error=166.562, avgs=0 070/300: dt: 0.9000, rms radial error=165.625, avgs=0 075/300: dt: 0.9000, rms radial error=164.694, avgs=0 080/300: dt: 0.9000, rms radial error=163.768, avgs=0 085/300: dt: 0.9000, rms radial error=162.846, avgs=0 090/300: dt: 0.9000, rms radial error=161.930, avgs=0 095/300: dt: 0.9000, rms radial error=161.019, avgs=0 100/300: dt: 0.9000, rms radial error=160.112, avgs=0 105/300: dt: 0.9000, rms radial error=159.211, avgs=0 110/300: dt: 0.9000, rms radial error=158.314, avgs=0 115/300: dt: 0.9000, rms radial error=157.422, avgs=0 120/300: dt: 0.9000, rms radial error=156.535, avgs=0 125/300: dt: 0.9000, rms radial error=155.654, avgs=0 130/300: dt: 0.9000, rms radial error=154.777, avgs=0 135/300: dt: 0.9000, rms radial error=153.906, avgs=0 140/300: dt: 0.9000, rms radial error=153.040, avgs=0 145/300: dt: 0.9000, rms radial error=152.179, avgs=0 150/300: dt: 0.9000, rms radial error=151.323, avgs=0 155/300: dt: 0.9000, rms radial error=150.471, avgs=0 160/300: dt: 0.9000, rms radial error=149.624, avgs=0 165/300: dt: 0.9000, rms radial error=148.782, avgs=0 170/300: dt: 0.9000, rms radial error=147.944, avgs=0 175/300: dt: 0.9000, rms radial error=147.111, avgs=0 180/300: dt: 0.9000, rms radial error=146.283, avgs=0 185/300: dt: 0.9000, rms radial error=145.459, avgs=0 190/300: dt: 0.9000, rms radial error=144.640, avgs=0 195/300: dt: 0.9000, rms radial error=143.825, avgs=0 200/300: dt: 0.9000, rms radial error=143.015, avgs=0 205/300: dt: 0.9000, rms radial error=142.209, avgs=0 210/300: dt: 0.9000, rms radial error=141.408, avgs=0 215/300: dt: 0.9000, rms radial error=140.611, avgs=0 220/300: dt: 0.9000, rms radial error=139.819, avgs=0 225/300: dt: 0.9000, rms radial error=139.031, avgs=0 230/300: dt: 0.9000, rms radial error=138.248, avgs=0 235/300: dt: 0.9000, rms radial error=137.468, avgs=0 240/300: dt: 0.9000, rms radial error=136.694, avgs=0 245/300: dt: 0.9000, rms radial error=135.923, avgs=0 250/300: dt: 0.9000, rms radial error=135.157, avgs=0 255/300: dt: 0.9000, rms radial error=134.396, avgs=0 260/300: dt: 0.9000, rms radial error=133.638, avgs=0 265/300: dt: 0.9000, rms radial error=132.885, avgs=0 270/300: dt: 0.9000, rms radial error=132.136, avgs=0 275/300: dt: 0.9000, rms radial error=131.391, avgs=0 280/300: dt: 0.9000, rms radial error=130.650, avgs=0 285/300: dt: 0.9000, rms radial error=129.914, avgs=0 290/300: dt: 0.9000, rms radial error=129.182, avgs=0 295/300: dt: 0.9000, rms radial error=128.453, avgs=0 300/300: dt: 0.9000, rms radial error=127.729, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16567.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2828.12 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 300.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00695 epoch 4 (K=640.0), pass 1, starting sse = 17.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.16/15 = 0.01060 final distance error %27.14 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 254.792749 mris_sphere stimesec 0.448848 mris_sphere ru_maxrss 212036 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 53237 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9840 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 5595 mris_sphere ru_nivcsw 3825 FSRUNTIME@ mris_sphere 0.0341 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy rh Wed Jul 11 01:23:13 UTC 2018 /out/freesurfer/sub-18042401/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology rh Wed Jul 11 01:23:13 UTC 2018 mris_fix_topology -rusage /out/freesurfer/sub-18042401/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-18042401 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-24 (nv=139790, nf=279628, ne=419442, g=13) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 2019 ambiguous faces found in tessellation segmenting defects... 24 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 13 23 defects to be corrected 0 vertices coincident reading input surface /out/freesurfer/sub-18042401/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1052 (-4.5526) -vertex loglikelihood: -5.7172 (-2.8586) -normal dot loglikelihood: -3.6641 (-3.6641) -quad curv loglikelihood: -6.4691 (-3.2346) Total Loglikelihood : -24.9556 CORRECTING DEFECT 0 (vertices=38, convex hull=29, v0=16878) After retessellation of defect 0 (v0=16878), euler #=-20 (138550,415137,276567) : difference with theory (-20) = 0 CORRECTING DEFECT 1 (vertices=16, convex hull=64, v0=35468) After retessellation of defect 1 (v0=35468), euler #=-19 (138557,415180,276604) : difference with theory (-19) = 0 CORRECTING DEFECT 2 (vertices=5, convex hull=15, v0=38417) After retessellation of defect 2 (v0=38417), euler #=-18 (138558,415187,276611) : difference with theory (-18) = 0 CORRECTING DEFECT 3 (vertices=10, convex hull=23, v0=41093) After retessellation of defect 3 (v0=41093), euler #=-17 (138559,415194,276618) : difference with theory (-17) = 0 CORRECTING DEFECT 4 (vertices=24, convex hull=26, v0=51240) After retessellation of defect 4 (v0=51240), euler #=-16 (138564,415214,276634) : difference with theory (-16) = 0 CORRECTING DEFECT 5 (vertices=284, convex hull=226, v0=51281) normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 4 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 4 faces normal vector of length zero at vertex 138827 with 4 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces normal vector of length zero at vertex 138827 with 3 faces After retessellation of defect 5 (v0=51281), euler #=-15 (138601,415426,276810) : difference with theory (-15) = 0 CORRECTING DEFECT 6 (vertices=5, convex hull=29, v0=55320) After retessellation of defect 6 (v0=55320), euler #=-14 (138602,415438,276822) : difference with theory (-14) = 0 CORRECTING DEFECT 7 (vertices=9, convex hull=25, v0=55363) After retessellation of defect 7 (v0=55363), euler #=-13 (138605,415453,276835) : difference with theory (-13) = 0 CORRECTING DEFECT 8 (vertices=10, convex hull=19, v0=63161) After retessellation of defect 8 (v0=63161), euler #=-12 (138607,415466,276847) : difference with theory (-12) = 0 CORRECTING DEFECT 9 (vertices=271, convex hull=114, v0=69053) After retessellation of defect 9 (v0=69053), euler #=-11 (138659,415685,277015) : difference with theory (-11) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=30, v0=94178) After retessellation of defect 10 (v0=94178), euler #=-10 (138663,415707,277034) : difference with theory (-10) = 0 CORRECTING DEFECT 11 (vertices=56, convex hull=111, v0=98398) After retessellation of defect 11 (v0=98398), euler #=-9 (138672,415788,277107) : difference with theory (-9) = 0 CORRECTING DEFECT 12 (vertices=22, convex hull=34, v0=103020) After retessellation of defect 12 (v0=103020), euler #=-8 (138678,415816,277130) : difference with theory (-8) = 0 CORRECTING DEFECT 13 (vertices=60, convex hull=109, v0=103060) After retessellation of defect 13 (v0=103060), euler #=-6 (138688,415891,277197) : difference with theory (-7) = -1 CORRECTING DEFECT 14 (vertices=30, convex hull=43, v0=104961) After retessellation of defect 14 (v0=104961), euler #=-6 (138697,415940,277237) : difference with theory (-6) = 0 CORRECTING DEFECT 15 (vertices=29, convex hull=87, v0=109661) After retessellation of defect 15 (v0=109661), euler #=-5 (138705,415997,277287) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=11, convex hull=22, v0=111856) After retessellation of defect 16 (v0=111856), euler #=-4 (138708,416012,277300) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=34, convex hull=34, v0=111908) After retessellation of defect 17 (v0=111908), euler #=-3 (138717,416052,277332) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=11, convex hull=15, v0=113325) After retessellation of defect 18 (v0=113325), euler #=-2 (138719,416062,277341) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=93, convex hull=56, v0=119054) After retessellation of defect 19 (v0=119054), euler #=-1 (138733,416130,277396) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=40, convex hull=34, v0=131578) After retessellation of defect 20 (v0=131578), euler #=0 (138734,416146,277412) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=36, convex hull=59, v0=136552) After retessellation of defect 21 (v0=136552), euler #=1 (138747,416208,277462) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=124, convex hull=58, v0=138742) After retessellation of defect 22 (v0=138742), euler #=2 (138760,416274,277516) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.07-->9.26) (max @ vno 53664 --> 55151) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.07-->9.26) (max @ vno 53664 --> 55151) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 100 mutations (40.2%), 149 crossovers (59.8%), 156 vertices were eliminated building final representation... 1030 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138760, nf=277516, ne=416274, g=0) writing corrected surface to /out/freesurfer/sub-18042401/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.8 minutes 0 defective edges removing intersecting faces 000: 148 intersecting 001: 7 intersecting mris_fix_topology utimesec 712.186340 mris_fix_topology stimesec 0.224992 mris_fix_topology ru_maxrss 435576 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 109874 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13048 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 1037 mris_fix_topology ru_nivcsw 833 FSRUNTIME@ mris_fix_topology rh 0.1967 hours 1 threads mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 138760 - 416274 + 277516 = 2 --> 0 holes F =2V-4: 277516 = 277520-4 (0) 2E=3F: 832548 = 832548 (0) total defect index = 0 /out/freesurfer/sub-18042401/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 36 intersecting 001: 8 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Jul 11 01:35:06 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-18042401 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /out/freesurfer/sub-18042401/mri/filled.mgz... reading volume /out/freesurfer/sub-18042401/mri/brain.finalsurfs.mgz... reading volume /out/freesurfer/sub-18042401/mri/../mri/aseg.presurf.mgz... reading volume /out/freesurfer/sub-18042401/mri/wm.mgz... 17340 bright wm thresholded. 20 bright non-wm voxels segmented. reading original surface position from /out/freesurfer/sub-18042401/surf/rh.orig... computing class statistics... border white: 263682 voxels (1.57%) border gray 287055 voxels (1.71%) WM (101.0): 100.8 +- 6.6 [70.0 --> 110.0] GM (81.0) : 79.7 +- 9.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.4 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 58.8 (was 40) setting MAX_GRAY to 98.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 49.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.00-->4.30) (max @ vno 53648 --> 53664) face area 0.28 +- 0.12 (0.00-->5.86) mean absolute distance = 0.76 +- 1.01 3635 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=78+-6.1 mean inside = 97.3, mean outside = 83.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=87.3, 56 (56) missing vertices, mean dist 0.2 [0.7 (%39.5)->0.8 (%60.5))] %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ef810, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.24 (0.08-->4.05) (max @ vno 53648 --> 53664) face area 0.28 +- 0.13 (0.00-->3.43) mean absolute distance = 0.38 +- 0.67 3136 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2195437.8, rms=7.791 001: dt: 0.5000, sse=1328187.8, rms=5.382 (30.921%) 002: dt: 0.5000, sse=951412.4, rms=3.873 (28.040%) 003: dt: 0.5000, sse=789551.1, rms=3.000 (22.533%) 004: dt: 0.5000, sse=717510.9, rms=2.507 (16.430%) 005: dt: 0.5000, sse=693970.5, rms=2.291 (8.634%) 006: dt: 0.5000, sse=681018.3, rms=2.182 (4.760%) rms = 2.15, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=675794.5, rms=2.151 (1.419%) 008: dt: 0.2500, sse=611655.0, rms=1.353 (37.110%) 009: dt: 0.2500, sse=604998.8, rms=1.231 (8.966%) rms = 1.21, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=601559.2, rms=1.206 (2.070%) rms = 1.19, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=600441.8, rms=1.189 (1.373%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.4, 64 (27) missing vertices, mean dist -0.2 [0.4 (%68.8)->0.3 (%31.2))] %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ef810, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.23 (0.10-->3.94) (max @ vno 53648 --> 53664) face area 0.35 +- 0.16 (0.00-->4.31) mean absolute distance = 0.30 +- 0.46 3755 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1034695.7, rms=3.538 012: dt: 0.5000, sse=822856.3, rms=2.143 (39.418%) 013: dt: 0.5000, sse=779976.4, rms=1.769 (17.472%) 014: dt: 0.5000, sse=764666.6, rms=1.603 (9.363%) rms = 1.67, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=741475.6, rms=1.273 (20.589%) 016: dt: 0.2500, sse=731348.9, rms=1.105 (13.222%) rms = 1.06, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=729188.7, rms=1.063 (3.806%) rms = 1.05, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=728111.2, rms=1.047 (1.507%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=91.4, 97 (24) missing vertices, mean dist -0.2 [0.3 (%72.3)->0.2 (%27.7))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ef810, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.10-->3.99) (max @ vno 138579 --> 58913) face area 0.34 +- 0.15 (0.00-->3.99) mean absolute distance = 0.23 +- 0.35 3964 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=892920.2, rms=2.846 019: dt: 0.5000, sse=756591.7, rms=1.685 (40.783%) 020: dt: 0.5000, sse=740003.9, rms=1.517 (9.965%) 021: dt: 0.5000, sse=736106.8, rms=1.448 (4.530%) rms = 1.61, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=710181.8, rms=1.096 (24.318%) 023: dt: 0.2500, sse=703888.3, rms=0.963 (12.195%) rms = 0.95, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=705171.1, rms=0.952 (1.098%) rms = 0.94, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=701709.4, rms=0.944 (0.837%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.2, 107 (22) missing vertices, mean dist -0.1 [0.3 (%58.8)->0.2 (%41.2))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ef810, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /out/freesurfer/sub-18042401/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=714754.1, rms=1.417 026: dt: 0.5000, sse=690667.7, rms=0.947 (33.161%) rms = 1.19, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=679861.6, rms=0.793 (16.238%) rms = 0.77, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=678805.9, rms=0.767 (3.330%) rms = 0.76, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=676553.1, rms=0.756 (1.475%) positioning took 0.4 minutes generating cortex label... 12 non-cortical segments detected only using segment with 6866 vertices erasing segment 0 (vno[0] = 45913) erasing segment 2 (vno[0] = 56516) erasing segment 3 (vno[0] = 58932) erasing segment 4 (vno[0] = 102365) erasing segment 5 (vno[0] = 104016) erasing segment 6 (vno[0] = 104058) erasing segment 7 (vno[0] = 106001) erasing segment 8 (vno[0] = 107052) erasing segment 9 (vno[0] = 107948) erasing segment 10 (vno[0] = 108714) erasing segment 11 (vno[0] = 111667) writing cortex label to /out/freesurfer/sub-18042401/label/rh.cortex.label... writing curvature file /out/freesurfer/sub-18042401/surf/rh.curv writing smoothed area to rh.area writing curvature file /out/freesurfer/sub-18042401/surf/rh.area vertex spacing 0.88 +- 0.24 (0.02-->4.01) (max @ vno 58913 --> 138579) face area 0.33 +- 0.15 (0.00-->3.74) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 rh Wed Jul 11 01:39:20 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Jul 11 01:39:25 UTC 2018 /out/freesurfer/sub-18042401/scripts mris_inflate -rusage /out/freesurfer/sub-18042401/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.7 mm, total surface area = 82869 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.3 minutes mris_inflate utimesec 42.980127 mris_inflate stimesec 0.362916 mris_inflate ru_maxrss 210188 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 52808 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10856 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2378 mris_inflate ru_nivcsw 672 #-------------------------------------------- #@# Curv .H and .K rh Wed Jul 11 01:39:45 UTC 2018 /out/freesurfer/sub-18042401/surf mris_curvature -w rh.white.preaparc total integrated curvature = 5.417*4pi (68.073) --> -4 handles ICI = 152.3, FI = 1696.3, variation=26280.079 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H Linux ef810ab26e4e 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018 For more details, see the log file /out/freesurfer/sub-18042401/scripts/recon-all-rh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Standard error: ln: failed to create symbolic link 'rh.white.H': Operation not supported Return code: 1 180711-01:39:51,447 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:51,452 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:54,738 cli WARNING: Errors occurred while generating reports for participants: 18042401 (2). fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues bash-4.2$